Alignments for a candidate for lpd in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Echinicola vietnamensis KMM 6221, DSM 17526

Align Dihydrolipoyl dehydrogenase 1, mitochondrial; AtmLPD1; mtLPD1; Dihydrolipoamide dehydrogenase 1; Glycine cleavage system L protein 1; Pyruvate dehydrogenase complex E3 subunit 1; E3-1; PDC-E3 1; EC 1.8.1.4 (characterized)
to candidate Echvi_0770 Echvi_0770 dihydrolipoamide dehydrogenase

Query= SwissProt::Q9M5K3
         (507 letters)



>FitnessBrowser__Cola:Echvi_0770
          Length = 494

 Score =  482 bits (1240), Expect = e-140
 Identities = 239/464 (51%), Positives = 338/464 (72%), Gaps = 2/464 (0%)

Query: 45  DVVIIGGGPGGYVAAIKASQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           D+++IG GPGGYVAAI+ +QLG+KT  +EK   LGGTCLNVGCIPSKALL SS  YH A 
Sbjct: 32  DLIVIGSGPGGYVAAIRGAQLGMKTAIVEKYPTLGGTCLNVGCIPSKALLDSSEHYHNAA 91

Query: 105 HSFANHGIKVSSVEVDLPAMLAQKDNAVKNLTRGIEGLFKKNKVTYVKGYGKFISPNEVS 164
           H+F  HGI +  ++V+L  M+++KD+ VK    GI  L KKNK+   +G G F+  N V 
Sbjct: 92  HTFKTHGIDLKDLKVNLKQMISRKDDVVKQNVDGISYLMKKNKIDVHQGVGSFVDKNTVK 151

Query: 165 VETIDGGNTIVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLSEVPKKLIVIGAGY 224
           V   DG +T + G++II+ATGS   SLP I ID+K++++ST AL + EVPK++IVIG G 
Sbjct: 152 VTKDDGKSTEITGENIIIATGSKPASLPFIEIDKKRVITSTEALKMKEVPKRMIVIGGGV 211

Query: 225 IGLEMGSVWGRLGSEVTVVEFAGDIVPSMDGEIRKQFQRSLEKQKMKFMLKTKVVSVDSS 284
           IG+E+GSV+ R+G++V+VVEF   ++PSMD  + K+ Q+SL+K   +F LK KV +V S+
Sbjct: 212 IGMELGSVYARMGAKVSVVEFMDSLIPSMDKTMGKELQKSLKKLGFEFYLKHKVTAVKST 271

Query: 285 SDGVKLTVEPAEGGEQSILEADVVLVSAGRTPFTSGLDLEKIGVETDKAGRILVNDRFLS 344
           +  V +T E ++G E  + + D VLVS GR P+T GL+ E  GV+ +  G++ V++   +
Sbjct: 272 AKEVTVTAENSKGEEVQV-KGDYVLVSIGRKPYTEGLNPEAAGVKVNDRGQVEVDEHLKT 330

Query: 345 NVPGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTHPEVASVGKT 404
           +   +YAIGDV+ G MLAHKAEE+GV   E +AG+  H++Y+ +PGVVYT PEVA+VG +
Sbjct: 331 SADNIYAIGDVVKGAMLAHKAEEEGVLVAEQLAGQKPHINYNLIPGVVYTWPEVAAVGYS 390

Query: 405 EEQLKKEGVSYRVGKFPFMANSRAKAIDNAEGLVKILADKETDKILGVHIMAPNAGELIH 464
           EEQLK++G+ Y+ GKFPFMA+ RA+A  + +GLVK+LAD ETD+ILGVH++ P   ++I 
Sbjct: 391 EEQLKEKGIKYKTGKFPFMASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIA 450

Query: 465 EAVLAINYDASSEDIARVCHAHPTMSEALKEAAM-ATYDKPIHI 507
           EAV+A+ Y AS+EDIAR+ HAHPT +EA KEA + AT ++ +H+
Sbjct: 451 EAVVAMEYRASAEDIARMSHAHPTYTEAFKEACLAATENRALHV 494


Lambda     K      H
   0.315    0.133    0.375 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 600
Number of extensions: 21
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 507
Length of database: 494
Length adjustment: 34
Effective length of query: 473
Effective length of database: 460
Effective search space:   217580
Effective search space used:   217580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate Echvi_0770 Echvi_0770 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01350.hmm
# target sequence database:        /tmp/gapView.2459.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01350  [M=461]
Accession:   TIGR01350
Description: lipoamide_DH: dihydrolipoyl dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                            Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
     7e-182  591.1  13.5   7.9e-182  590.9  13.5    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0770  Echvi_0770 dihydrolipoamide dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0770  Echvi_0770 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.9  13.5  7.9e-182  7.9e-182       2     457 ..      31     489 ..      30     494 .] 0.97

  Alignments for each domain:
  == domain 1  score: 590.9 bits;  conditional E-value: 7.9e-182
                            TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgievenv 73 
                                          yd++viG+GpgGYvaAir aqlg+k+a+vek  +lGGtClnvGCiP+KalL s+e ++++ + +k++gi+++++
  lcl|FitnessBrowser__Cola:Echvi_0770  31 YDLIVIGSGPGGYVAAIRGAQLGMKTAIVEKyPTLGGTCLNVGCIPSKALLDSSEHYHNAAHtFKTHGIDLKDL 104
                                          9******************************99***************************************** PP

                            TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGseprel 146
                                          k++l+++  rk+ vvk+ v+G+++L+kknk++v++G ++++dk++v+v+k++++ ++++ +niiiAtGs+p++l
  lcl|FitnessBrowser__Cola:Echvi_0770 105 KVNLKQMISRKDDVVKQNVDGISYLMKKNKIDVHQGVGSFVDKNTVKVTKDDGKsTEITGENIIIATGSKPASL 178
                                          **************************************************998878899*************** PP

                            TIGR01350 147 plkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkk 220
                                          p+ +e d+k+vits+eal++kevp++++++GgGviG+E++s++a++G+kv+v+e++d ++p +d+++ k+l+k+
  lcl|FitnessBrowser__Cola:Echvi_0770 179 PF-IEIDKKRVITSTEALKMKEVPKRMIVIGGGVIGMELGSVYARMGAKVSVVEFMDSLIPSMDKTMGKELQKS 251
                                          **.*********************************************************************** PP

                            TIGR01350 221 lkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgveldergaikvd 292
                                          lkk g +++ ++kvt+v+++++ev+v+a+++  e+ ++++++vLv++Grkp +e+l+ e+ gv++++rg+++vd
  lcl|FitnessBrowser__Cola:Echvi_0770 252 LKKLGFEFYLKHKVTAVKSTAKEVTVTAENSkgEEVQVKGDYVLVSIGRKPYTEGLNPEAAGVKVNDRGQVEVD 325
                                          **********************999554443358899************************************* PP

                            TIGR01350 293 eelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeeg 366
                                          e+l+t++++iyaiGDv++++mLAh+A++egv++ae++ag+++ +i+y+++P v+yt Peva+vG++eeq+ke+g
  lcl|FitnessBrowser__Cola:Echvi_0770 326 EHLKTSADNIYAIGDVVKGAMLAHKAEEEGVLVAEQLAGQKP-HINYNLIPGVVYTWPEVAAVGYSEEQLKEKG 398
                                          ***************************************998.9****************************** PP

                            TIGR01350 367 ievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpH 440
                                          i++k+gkfpf+a+g+a+a+ +tdG+vkv++d +t+eilG+h++g++ +++i+e+++a+e ++++e++a++ h+H
  lcl|FitnessBrowser__Cola:Echvi_0770 399 IKYKTGKFPFMASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIAEAVVAMEYRASAEDIARMSHAH 472
                                          ************************************************************************** PP

                            TIGR01350 441 PtlsEaikeaalaalgk 457
                                          Pt++Ea+kea+laa+++
  lcl|FitnessBrowser__Cola:Echvi_0770 473 PTYTEAFKEACLAATEN 489
                                          ***********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (494 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.09
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources